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153 results on '"Pierre Lefeuvre"'

1. Characterization of Six Ampeloviruses Infecting Pineapple in Reunion Island Using a Combination of High-Throughput Sequencing Approaches

Author: Delphine Massé, Thierry Candresse, Denis Filloux, Sébastien Massart, Nathalie Cassam, Bruno Hostachy, Armelle Marais, Emmanuel Fernandez, Philippe Roumagnac, Eric Verdin, Pierre-Yves Teycheney, Jean-Michel Lett, and Pierre Lefeuvre
Subjects: Ananas comosus, pineapple mealybug wilt-associated viruses, ampelovirus, high-throughput sequencing, short and long reads, molecular diversity, Microbiology, QR1-502
Abstract: The cultivation of pineapple (Ananas comosus) is threatened worldwide by mealybug wilt disease of pineapple (MWP), whose etiology is not yet fully elucidated. In this study, we characterized pineapple mealybug wilt-associated ampeloviruses (PMWaVs, family Closteroviridae) from a diseased pineapple plant collected from Reunion Island, using a high-throughput sequencing approach combining Illumina short reads and Nanopore long reads. Reads co-assembly resulted in complete or near-complete genomes for six distinct ampeloviruses, including the first complete genome of pineapple mealybug wilt-associated virus 5 (PMWaV5) and that of a new species tentatively named pineapple mealybug wilt-associated virus 7 (PMWaV7). Short reads data provided high genome coverage and sequencing depths for all six viral genomes, contrary to long reads data. The 5′ and 3′ ends of the genome for most of the six ampeloviruses could be recovered from long reads, providing an alternative to RACE-PCRs. Phylogenetic analyses did not unveil any geographic structuring of the diversity of PMWaV1, PMWaV2 and PMWaV3 isolates, supporting the current hypothesis that PMWaVs were mainly spread by human activity and vegetative propagation.
Published: 2024
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2. Geographic population structure of the honeybee microsporidian parasite Vairimorpha (Nosema) ceranae in the South West Indian Ocean

Author: Nicolas Blot, Johanna Clémencet, Cyril Jourda, Pierre Lefeuvre, Natapot Warrit, Olivier Esnault, and Hélène Delatte
Subjects: Medicine, Science
Abstract: Abstract The microsporidian Vairimorpha (Nosema) ceranae is one of the most common parasites of the honeybee. A single honeybee carries many parasites and therefore multiple alleles of V. ceranae genes that seem to be ubiquitous. As a consequence, nucleotide diversity analyses have not allowed discriminating genetic structure of parasite populations. We performed deep loci-targeted sequencing to monitor the haplotype frequencies of genome markers in isolates from discontinuous territories, namely the tropical islands of the South West Indian Ocean. The haplotype frequency distribution corroborated the suspected tetraploidy of the parasite. Most major haplotypes were ubiquitous in the area but with variable frequency. While oceanic isolates differed from European and Asian outgroups, parasite populations from distinct archipelagoes also differed in their haplotype distribution. Interestingly an original and very divergent Malagasy isolate was detected. The observed population structure allowed formulating hypotheses upon the natural history of V. ceranae in this oceanic area. We also discussed the usefulness of allelic distribution assessment, using multiple informative loci or genome-wide analyses, when parasite population is not clonal within a single host.
Published: 2023
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3. Study of neck formation and densification in porous hydroxyapatite ceramics using thermal conductivity measurements

Author: David S. Smith, Pierre Lefeuvre, Maxence Renaux, Benoit Nait-Ali, and Anne Leriche
Subjects: Hydroxyapatite ceramics, Green bodies, Thermal conductivity, Sintering, Neck formation, Clay industries. Ceramics. Glass, TP785-869
Abstract: Neck formation and densification during sintering have strong effects on the thermal conductivity of a porous ceramic body. This has been described by an analytical model using grain conductivity, grain size, pore fraction and particle – particle contact area as input parameters. It has been tested on hydroxyapatite ceramics sintered with conventional, microwave and spark plasma techniques. The green bodies containing at least 40% porosity yield conductivity values in the range 0.24–0.29 Wm−1K−1. Neck formation in the initial stage of sintering increases the values to above 0.5 Wm−1K−1. Further increase is achieved by densification, well described by Landauer's relation as part of the model with close agreement to experiment for hydroxyapatite ceramics containing 40 to 5% porosity. An evaluation of thermal conductivity for 100% dense hydroxyapatite gives a value of 1.5 Wm−1K−1 which is almost constant between room temperature and 900 °C.
Published: 2023
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4. Synergy between an emerging monopartite begomovirus and a DNA-B component

Author: Alassane Ouattara, Fidèle Tiendrébéogo, Nathalie Becker, Cica Urbino, Gaël Thébaud, Murielle Hoareau, Agathe Allibert, Frédéric Chiroleu, Marie-Stéphanie Vernerey, Edgar Valentin Traoré, Nicolas Barro, Oumar Traoré, Pierre Lefeuvre, and Jean-Michel Lett
Subjects: Medicine, Science
Abstract: Abstract In recent decades, a legion of monopartite begomoviruses transmitted by the whitefly Bemisia tabaci has emerged as serious threats to vegetable crops in Africa. Recent studies in Burkina Faso (West Africa) reported the predominance of pepper yellow vein Mali virus (PepYVMLV) and its frequent association with a previously unknown DNA-B component. To understand the role of this DNA-B component in the emergence of PepYVMLV, we assessed biological traits related to virulence, virus accumulation, location in the tissue and transmission. We demonstrate that the DNA-B component is not required for systemic movement and symptom development of PepYVMLV (non-strict association), but that its association produces more severe symptoms including growth arrest and plant death. The increased virulence is associated with a higher viral DNA accumulation in plant tissues, an increase in the number of contaminated nuclei of the phloem parenchyma and in the transmission rate by B. tabaci. Our results suggest that the association of a DNA-B component with the otherwise monopartite PepYVMLV is a key factor of its emergence.
Published: 2022
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5. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Author: Adrien Rieux, Paola Campos, Arnaud Duvermy, Sarah Scussel, Darren Martin, Myriam Gaudeul, Pierre Lefeuvre, Nathalie Becker, and Jean-Michel Lett
Subjects: Medicine, Science
Abstract: Abstract Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
Published: 2021
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6. Symptom evolution following the emergence of maize streak virus

Author: Adérito L Monjane, Simon Dellicour, Penelope Hartnady, Kehinde A Oyeniran, Betty E Owor, Marion Bezuidenhout, Daphné Linderme, Rizwan A Syed, Lara Donaldson, Shane Murray, Edward P Rybicki, Anders Kvarnheden, Elham Yazdkhasti, Pierre Lefeuvre, Rémy Froissart, Philippe Roumagnac, Dionne N Shepherd, Gordon W Harkins, Marc A Suchard, Philippe Lemey, Arvind Varsani, and Darren P Martin
Subjects: virulence, pathogenicity, evolutionary trade-off, chlorosis, Medicine, Science, Biology (General), QH301-705.5
Abstract: For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed. This demonstrates an evolutionary trade-off between amounts of pathogen-inflicted harm and how effectively viruses position themselves within plants to enable onward transmission.
Published: 2020
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7. New World Cactaceae Plants Harbor Diverse Geminiviruses

Author: Rafaela S. Fontenele, Andrew M. Salywon, Lucas C. Majure, Ilaria N. Cobb, Amulya Bhaskara, Jesús A. Avalos-Calleros, Gerardo R. Argüello-Astorga, Kara Schmidlin, Anthony Khalifeh, Kendal Smith, Joshua Schreck, Michael C. Lund, Matias Köhler, Martin F. Wojciechowski, Wendy C. Hodgson, Raul Puente-Martinez, Koenraad Van Doorslaer, Safaa Kumari, Kehinde A. Oyeniran, Christian Vernière, Denis Filloux, Philippe Roumagnac, Pierre Lefeuvre, Simone G. Ribeiro, Simona P. Kraberger, Darren P. Martin, and Arvind Varsani
Subjects: Cactaceae, Geminiviridae, Becurtovirus, recombination, diversity, Microbiology, QR1-502
Abstract: The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.
Published: 2021
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8. Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses

Author: Selim Ben Chehida, Denis Filloux, Emmanuel Fernandez, Oumaima Moubset, Murielle Hoareau, Charlotte Julian, Laurence Blondin, Jean-Michel Lett, Philippe Roumagnac, and Pierre Lefeuvre
Subjects: MinION, nanopore sequencing, rolling circle amplification, viral metagenomics, CRESS DNA, capulavirus, Biology (General), QH301-705.5
Abstract: Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible.
Published: 2021
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9. Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America

Author: Rafaela S. Fontenele, Amulya Bhaskara, Ilaria N. Cobb, Lucas C. Majure, Andrew M. Salywon, Jesús A. Avalos-Calleros, Gerardo R. Argüello-Astorga, Kara Schmidlin, Philippe Roumagnac, Simone G. Ribeiro, Simona Kraberger, Darren P. Martin, Pierre Lefeuvre, and Arvind Varsani
Subjects: Geminiviridae, begomovirus, pseudo-recombination, recombination, Microbiology, QR1-502
Abstract: Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.
Published: 2021
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10. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

Author: Rafaela S. Fontenele, Andrew M. Salywon, Lucas C. Majure, Ilaria N. Cobb, Amulya Bhaskara, Jesús A. Avalos-Calleros, Gerardo R. Argüello-Astorga, Kara Schmidlin, Anthony Khalifeh, Kendal Smith, Joshua Schreck, Michael C. Lund, Matias Köhler, Martin F. Wojciechowski, Wendy C. Hodgson, Raul Puente-Martinez, Koenraad Van Doorslaer, Safaa Kumari, Christian Vernière, Denis Filloux, Philippe Roumagnac, Pierre Lefeuvre, Simone G. Ribeiro, Simona Kraberger, Darren P. Martin, and Arvind Varsani
Subjects: geminivirus, Cactoideae, Opuntioideae, ssDNA virus, cochineal insects, Microbiology, QR1-502
Abstract: Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
Published: 2020
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11. Whole-genome sequence and analysis of Xanthomonas euvesicatoria strains and reassessment of the species

Author: Jeri D. Barak, Taca Vancheva, Pierre Lefeuvre, Jeffrey B. Jones, Sujan Timilsina, Gerald V. Minsavage, Gary E. Vallad, and Ralf Koebnik
Subjects: Comparative genomics, Taxonomy, Type III effectors, Cell wall degrading enzymes, Xanthomonas perforans, Xanthomonas euvesicatoria, Plant culture, SB1-1110
Abstract: Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 which was pathogenic on pepper but elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that these strains are all atypical to both X. euvesicatoria and X. perforans. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria as well. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic on various hosts. The results from this study support the finding that T3 effector repertoire and host range are fundamental for the study of host – microbe interaction but of little relevance to bacterial speciation.
Published: 2016
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12. Biological Invasions of Geminiviruses: Case Study of TYLCV and Bemisia tabaci in Reunion Island

Author: Jean-Michel Lett, Bernard Reynaud, Hélène Delatte, Nathalie Becker, Pierre Lefeuvre, Magali Thierry, and Frédéric Péréfarres
Subjects: biological invasion, Begomovirus, Tomato yellow leaf curl virus, Bemisia tabaci, endosymbionts, competition, Microbiology, QR1-502
Abstract: In the last 20 years, molecular ecology approaches have proven to be extremely useful to identify and assess factors associated with viral emerging diseases, particularly in economically and socially important tropical crops such as maize (maize streak disease) and cassava (cassava mosaic disease). Molecular ecology approaches were applied in Reunion Island to analyze the epidemic of tomato yellow leaf curl disease, which has been affecting the island since the end of the 1990s. Before the invasive biotype B (currently known as Middle East-Asia Minor 1 cryptic species) of Bemisia tabaci spread across the world, Reunion Island (South West Indian Ocean) only hosted an indigenous biotype of B. tabaci, Ms (currently known as Indian Ocean cryptic species). Wild hybrids between invasive and indigenous species were subsequently characterized over multiple generations. Endosymbiont analysis of the hybrid population indicated that matings were non-random. Similarly, while no indigenous begomoviruses have ever been reported on Reunion Island, the two main strains of one of the most damaging and emerging plant viruses in the world, the Mild and Israel strains of the Tomato yellow leaf curl virus (TYLCV-Mld and TYLCV-IL), were introduced in 1997 and 2004 respectively. While these introductions extensively modified the agricultural landscape of Reunion Island, they also provided an invaluable opportunity to study the ecological and genetic mechanisms involved in biological invasion and competition.
Published: 2012
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13. Recombination in Eukaryotic Single Stranded DNA Viruses

Author: Philippe Roumagnac, Arvind Varsani, Michael Golden, Pierre Lefeuvre, Darren P. Martin, and Philippe Biagini
Subjects: parvovirus, geminivirus, anellovirus, circovirus, nanovirus, Microbiology, QR1-502
Abstract: Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.
Published: 2011
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14. Cover cropping alters the diet of arthropods in a banana plantation: a metabarcoding approach.

Author: Gregory Mollot, Pierre-François Duyck, Pierre Lefeuvre, Françoise Lescourret, Jean-François Martin, Sylvain Piry, Elsa Canard, and Philippe Tixier
Subjects: Medicine, Science
Abstract: Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey.
Published: 2014
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15. Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

Author: Pierre Lefeuvre, Gilles Cellier, Benoît Remenant, Frédéric Chiroleu, and Philippe Prior
Subjects: Medicine, Science
Abstract: Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.
Published: 2013
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16. Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.

Author: Mario L Arrieta-Ortiz, Luis M Rodríguez-R, Álvaro L Pérez-Quintero, Lucie Poulin, Ana C Díaz, Nathalia Arias Rojas, Cesar Trujillo, Mariana Restrepo Benavides, Rebecca Bart, Jens Boch, Tristan Boureau, Armelle Darrasse, Perrine David, Thomas Dugé de Bernonville, Paula Fontanilla, Lionel Gagnevin, Fabien Guérin, Marie-Agnès Jacques, Emmanuelle Lauber, Pierre Lefeuvre, Cesar Medina, Edgar Medina, Nathaly Montenegro, Alejandra Muñoz Bodnar, Laurent D Noël, Juan F Ortiz Quiñones, Daniela Osorio, Carolina Pardo, Prabhu B Patil, Stéphane Poussier, Olivier Pruvost, Isabelle Robène-Soustrade, Robert P Ryan, Javier Tabima, Oscar G Urrego Morales, Christian Vernière, Sébastien Carrere, Valérie Verdier, Boris Szurek, Silvia Restrepo, Camilo López, Ralf Koebnik, and Adriana Bernal
Subjects: Medicine, Science
Abstract: Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
Published: 2013
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17. Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks.

Author: Darren P Martin, Pierre Lefeuvre, Arvind Varsani, Murielle Hoareau, Jean-Yves Semegni, Betty Dijoux, Claire Vincent, Bernard Reynaud, and Jean-Michel Lett
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range protein-protein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.
Published: 2011
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18. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome.

Author: Pierre Lefeuvre, Gordon W Harkins, Jean-Michel Lett, Rob W Briddon, Mark W Chase, Benoit Moury, and Darren P Martin
Subjects: Medicine, Science
Abstract: Despite having single stranded DNA genomes that are replicated by host DNA polymerases, viruses in the family Geminiviridae are apparently evolving as rapidly as some RNA viruses. The observed substitution rates of geminiviruses in the genera Begomovirus and Mastrevirus are so high that the entire family could conceivably have originated less than a million years ago (MYA). However, the existence of geminivirus related DNA (GRD) integrated within the genomes of various Nicotiana species suggests that the geminiviruses probably originated >10 MYA. Some have even suggested that a distinct New-World (NW) lineage of begomoviruses may have arisen following the separation by continental drift of African and American proto-begomoviruses ∼110 MYA. We evaluate these various geminivirus origin hypotheses using Bayesian coalescent-based approaches to date firstly the Nicotiana GRD integration events, and then the divergence of the NW and Old-World (OW) begomoviruses. Besides rejecting the possibility of a
Published: 2011
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19. The spread of tomato yellow leaf curl virus from the Middle East to the world.

Author: Pierre Lefeuvre, Darren P Martin, Gordon Harkins, Philippe Lemey, Alistair J A Gray, Sandra Meredith, Francisco Lakay, Adérito Monjane, Jean-Michel Lett, Arvind Varsani, and Jahangir Heydarnejad
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: The ongoing global spread of Tomato yellow leaf curl virus (TYLCV; Genus Begomovirus, Family Geminiviridae) represents a serious looming threat to tomato production in all temperate parts of the world. Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future movements of related viruses, determining the consequences of past TYLCV movements could reveal the ecological and economic risks associated with similar viral invasions. Towards this end we applied Bayesian phylogeographic inference and recombination analyses to available TYLCV sequences (including those of 15 new Iranian full TYLCV genomes) and reconstructed a plausible history of TYLCV's diversification and movements throughout the world. In agreement with historical accounts, our results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s (with 95% highest probability density intervals 1905-1972) and that the global spread of TYLCV only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains. Despite the global distribution of TYLCV we found no convincing evidence anywhere other than the Middle East and the Western Mediterranean of epidemiologically relevant TYLCV variants arising through recombination. Although the region around Iran is both the center of present day TYLCV diversity and the site of the most intensive ongoing TYLCV evolution, the evidence indicates that the region is epidemiologically isolated, which suggests that novel TYLCV variants found there are probably not direct global threats. We instead identify the Mediterranean basin as the main launch-pad of global TYLCV movements.
Published: 2010
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20. Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.

Author: Etienne Simon-Loriere, Roman Galetto, Meriem Hamoudi, John Archer, Pierre Lefeuvre, Darren P Martin, David L Robertson, and Matteo Negroni
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: The ability of pathogens to escape the host's immune response is crucial for the establishment of persistent infections and can influence virulence. Recombination has been observed to contribute to this process by generating novel genetic variants. Although distinctive recombination patterns have been described in many viral pathogens, little is known about the influence of biases in the recombination process itself relative to selective forces acting on newly formed recombinants. Understanding these influences is important for determining how recombination contributes to pathogen genome and proteome evolution. Most previous research on recombination-driven protein evolution has focused on relatively simple proteins, usually in the context of directed evolution experiments. Here, we study recombination in the envelope gene of HIV-1 between primary isolates belonging to subtypes that recombine naturally in the HIV/AIDS pandemic. By characterizing the early steps in the generation of recombinants, we provide novel insights into the evolutionary forces that shape recombination patterns within viral populations. Specifically, we show that the combined effects of mechanistic processes that determine the locations of recombination breakpoints across the HIV-1 envelope gene, and purifying selection acting against dysfunctional recombinants, can explain almost the entire distribution of breakpoints found within this gene in nature. These constraints account for the surprising paucity of recombination breakpoints found in infected individuals within this highly variable gene. Thus, the apparent randomness of HIV evolution via recombination may in fact be relatively more predictable than anticipated. In addition, the dominance of purifying selection in localized areas of the HIV genome defines regions where functional constraints on recombinants appear particularly strong, pointing to vulnerable aspects of HIV biology.
Published: 2009
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21. Avoidance of protein fold disruption in natural virus recombinants.

Author: Pierre Lefeuvre, Jean-Michel Lett, Bernard Reynaud, and Darren P Martin
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: With the development of reliable recombination detection tools and an increasing number of available genome sequences, many studies have reported evidence of recombination in a wide range of virus genera. Recombination is apparently a major mechanism in virus evolution, allowing viruses to evolve more quickly by providing immediate direct access to many more areas of a sequence space than are accessible by mutation alone. Recombination has been widely described amongst the insect-transmitted plant viruses in the genus Begomovirus (family Geminiviridae), with potential recombination hot- and cold-spots also having been identified. Nevertheless, because very little is understood about either the biochemical predispositions of different genomic regions to recombine or what makes some recombinants more viable than others, the sources of the evolutionary and biochemical forces shaping distinctive recombination patterns observed in nature remain obscure. Here we present a detailed analysis of unique recombination events detectable in the DNA-A and DNA-A-like genome components of bipartite and monopartite begomoviruses. We demonstrate both that recombination breakpoint hot- and cold-spots are conserved between the two groups of viruses, and that patterns of sequence exchange amongst the genomes are obviously non-random. Using a computational technique designed to predict structural perturbations in chimaeric proteins, we demonstrate that observed recombination events tend to be less disruptive than sets of simulated ones. Purifying selection acting against natural recombinants expressing improperly folded chimaeric proteins is therefore a major determinant of natural recombination patterns in begomoviruses.
Published: 2007
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22. L’hébergement Airbnb hors des grandes métropoles

Author: Nicolas Oppenchaim, Marie-Pierre Lefeuvre, and Julian Devaux
Subjects: Communication, Electrical and Electronic Engineering
Published: 2023

23. First report of chayote yellow mosaic virus in Côte d’Ivoire: a divergent strain infecting bitter melon

Author: Anthelme-Jocelin N’cho, Koutoua Séka, Murielle Hoareau, Pierre Lefeuvre, Marie-France Kouadio, Lassina Fondio, Daouda Koné, Germain Ochou, Hortense Diallo, Thibaud Martin, Jean-Michel Lett, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nangui Abrogoua (UNA), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Félix Houphouët-Boigny (UFHB), Centre National de la Recherche Agronomique - CNRA (IVORY COAST), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), This study was funded by the European Union (ERDF, contract GURDT I2016-1731–0006632), the Conseil Régional de la Réunion and CIRAD, and was conducted at the Plant Protection Platform (3P, IBISA). Jocelin N’cho is funded by a PhD fellowship from the French Ministry of Foreign Affairs via the C2D fund ‘Contrat de Désendettement et de Développement, Volet N°2 de recherche du projet AMRUGE-CI 2 (Appui à la Modernisation et à la Réforme des Universités et Grandes Ecoles de Côte d’Ivoire)’ through the project entitled ‘Adaptation et Développement de la culture protégée dans les conditions climatiques de la Côte d’Ivoire (HortiNet-CI)’., and European Project: ED431G2019/06,ERDF
Subjects: Identification, Indexage des virus des plantes, Sechium edule, Momordica charantia, [SDV]Life Sciences [q-bio], Plant Science, Virus des végétaux, Bitter melon, Geminiviridae, Cote d'Ivoire, Begomovirus, West Africa, Agronomy and Crop Science, Géminivirus, H20 - Maladies des plantes
Abstract: International audience; In this report, we present the first description of nine complete genome sequences of a new strain of chayote yellow mosaic virus (ChaYMV, genus Begomovirus, family Geminiviridae), provisionally named Cote d'Ivoire (ChaYMV-CI), isolated from bitter melon (Momordica charantia) leaf samples showing yellow mosaic symptoms collected in the region of Abidjan in Cote d'Ivoire in 2013 and 2019. The nucleotide sequences of ChaYMV-CI DNA-A-like genome share the highest nucleotide sequence identities (91.8-92.5%) with those of ChaYMV isolates from Benin and Cameroon. Phylogenetic analysis confirmed the segregation of ChaYMV isolates into two distinct clades and their affiliation to Old World monopartite begomoviruses. The discovery of a new strain of ChaYMV in West Africa, at the limit of the taxonomic demarcation threshold for begomoviruses (91%), call for further investigations into the molecular diversity, geographical distribution and host range of ChaYMV in Western Africa.
Published: 2022

24. Identification of a novel vitivirus from pineapple in Reunion Island

Author: Delphine Massé, Denis Filloux, Thierry Candresse, Sébastien Massart, Armelle Marais, Eric Verdin, Nathalie Cassam, Emmanuel Fernandez, Philippe Roumagnac, Pierre-Yves Teycheney, Pierre Lefeuvre, Jean-Michel Lett, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité Ravageurs et agents pathogènes tropicaux (RAPT), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche TERRA [Gembloux], Gembloux Agro-Bio Tech [Gembloux], Université de Liège-Université de Liège, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Conseil Régional de La Réunion, Anses, CIRAD, European Project, Conseil Regional de La Reunion, Cirad, and European Project: ERDF
Subjects: Phylogénie, Séquence nucléotidique, Genome, Viral, Ananas, Open Reading Frames, phytopathogenic virus, Virology, RNA, Messenger, Phylogeny, H20 - Maladies des plantes, Plant Diseases, Génome, Pineapple, High-Throughput Nucleotide Sequencing, General Medicine, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Vitivirus, Reunion Island, RNA, RNA, Viral, Ananas (genre), Capsid Proteins, Flexiviridae, Reunion
Abstract: We report the complete genome sequencing of a novel member of the genus Vitivirus in the family Betaflexiviridae (subfamily Trivirinae) infecting pineapple. The full genome of this virus was obtained from total RNAs extracted from pineapple leaf samples collected in Reunion Island, using a combination of high-throughput sequencing technologies. It is 6,757 nt long, excluding the poly(A) tail, and shares all the hallmarks of vitiviruses. Phylogenetic analyses performed on the replication-associated protein and capsid protein gene sequences unambiguously place this new virus, for which we propose the name “pineapple vitivirus A”, in the Vitivirus genus.
Published: 2022

25. La sociologie urbaine française : l’ouverture comme identité ?

Author: Alain Bourdin and Marie-Pierre Lefeuvre
Subjects: 050402 sociology, 0504 sociology, 05 social sciences, 050602 political science & public administration, General Social Sciences, 0506 political science
Abstract: Cet article presente un etat des lieux de la sociologie urbaine francaise fonde sur l’analyse thematique d’un corpus de 405 articles parus dans 8 revues entre 1990 et 2018. Il montre que la sociologie urbaine dispose d’un cœur faible. Elle est largement produite par des non-specialistes du domaine, s’interroge peu sur elle-meme et est peu cumulative. Si elle parait s’affaiblir au contact d’autres disciplines et du debat public, elle participe activement a des debats centraux de la discipline, sur les classes sociales en particulier. Elle est surtout alimentee par de tres nombreux travaux qui suivent une demarche exploratoire d’inspiration anthropologique. Paradoxalement, les tendances qui menacent sa coherence et sa cohesion lui conferent egalement un dynamisme propre.
Published: 2020

26. Sorghum mastrevirus-associated alphasatellites: new geminialphasatellites associated with an African streak mastrevirus infecting wild Poaceae plants on Reunion Island

Author: Sohini Claverie, Arvind Varsani, Pierre Lefeuvre, Jean-Michel Lett, Philippe Roumagnac, Denis Filloux, Murielle Hoareau, Darren P. Martin, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Arizona State University [Tempe] (ASU), University of Cape Town, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union (EU) : GURDT I2016-1731-0006632, Agropolis Fondation (Labex Agro - Montpellier, E-SPACE project) : 1504-004, Conseil Regional de la Reunion, CIRAD, and Agropolis Fondation (E-SPACE)
Subjects: Séquence nucléotidique, Subfamily, [SDV]Life Sciences [q-bio], Genome, Viral, Poaceae, Zea mays, Sorghum arundinaceum, Genome, 03 medical and health sciences, Mastrevirus, Genus, Virology, Maize streak virus, Alphasatellite, Phylogeny, Sorghum, Géminivirus, Plant Diseases, H20 - Maladies des plantes, 030304 developmental biology, Genetics, 0303 health sciences, Génome, biology, 030306 microbiology, Sequence Analysis, DNA, General Medicine, biology.organism_classification, Geminiviridae, Reunion
Abstract: Nine complete nucleotide sequences of geminialphasatellites (subfamily Geminialphasatellitinae, family Alphasatellitidae) recovered from the wild Poaceae Sorghum arundinaceum collected in Reunion are described and analyzed. While the helper geminivirus was identified as an isolate of maize streak virus (genus Mastrevirus, family Geminiviridae), the geminialphasatellite genomes were most closely related to, and shared ~63% identity with, clecrusatellites. Even though the geminialphasatellite molecules lack an adenine rich-region, they have the typical size of geminialphasatellites, encode a replication-associated protein in the virion sense, and have probable stem-loop structures at their virion-strand origins of replication. According to the proposed geminialphasatellite species and genus demarcation thresholds (88% and 70% nucleotide identity, respectively), the genomes identified here represent a new species (within a new genus) for which we propose the name "Sorghum mastrevirus-associated alphasatellite" (genus "Sorgasalphasatellite").
Published: 2020

27. A network approach to decipher the dynamics of Lysobacteraceae plasmid gene sharing

Author: Damien Richard, Philippe Roumagnac, Olivier Pruvost, Pierre Lefeuvre, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Union (ERDF contract GURDT I2016-1731-0006632), Conseil Regional de La Reunion, ANSES and CIRAD provided financial support, Agropolis Fondation (Labex Agro -Montpellier, E--SPACE project no. 1504--004), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Résistance génétique, Xanthomonas, Pouvoir pathogène, Plasmide, Xanthomonas campestris citri, Xanthomonas campestris, F30 - Génétique et amélioration des plantes, network of gene sharing, Lysobacteraceae, plasmid, Genetics, Dynamique des populations, Ecology, Evolution, Behavior and Systematics, Transfert de gène, Xylella fastidiosa, [SDV.GEN]Life Sciences [q-bio]/Genetics, Bacteria, Réseau, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Tolérance, horizontal gene transfer, U60 - Sciences de la vie et de la Terre
Abstract: International audience; Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The bacterial family Lysobacteraceae includes plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid-mediated adaptation has been reported. We searched for homologues of plasmid gene sequences from this family in the entire diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the family Lysobacteraceae, taxonomy strongly defined the boundaries of these exchanges, which only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically closely related taxa. We detected multiple plasmid-chromosome gene transfers, including the known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped substructures of isolates colonizing specific ecological niches and harbouring specific types of resistance genes. Genes associated with pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding of how this reservoir fuels the emergence and the spread of genes among this family and its potential impact on plant, animal and human health.
Published: 2022

28. New World Cactaceae Plants Harbor Diverse Geminiviruses

Author: Gerardo R. Argüello-Astorga, Arvind Varsani, Michael C. Lund, Simona Kraberger, Pierre Lefeuvre, Joshua Schreck, Denis Filloux, Anthony Khalifeh, Simone G. Ribeiro, Raul Puente-Martinez, Jesús Aarón Avalos-Calleros, Andrew M. Salywon, Safaa G. Kumari, Philippe Roumagnac, Kehinde A. Oyeniran, Kara Schmidlin, Rafaela S. Fontenele, Lucas C. Majure, Amulya Bhaskara, Wendy C. Hodgson, Martin F. Wojciechowski, Matias Köhler, Darren P. Martin, Kendal Smith, Koenraad Van Doorslaer, Christian Vernière, Ilaria N. Cobb, Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Desert Botanical Garden, Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), University of British Columbia [Vancouver], University of Texas at Dallas [Richardson] (UT Dallas), School of Behavioral and Brain Sciences, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Laboratório de Estudos em Vegetação Campestre (LEVCamp), Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, School of Animal and Comparative Biomedical Sciences, University of Arizona, Arizona Cancer Center, International Center for Agricultural Research in the Dry Areas (ICARDA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Cape Town, Institute of Infectious Diseases and Moleculare MedicineComputational Biolohy Group, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Embrapa Recursos Genéticos e Biotecnologia [Brasília], Structural Biology Research Unit, Department of Clinical Laboratory Sciences, The molecular work was supported by a start-up grant awarded to A.V. from Arizona State University, USA., RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, ANDREW M. SALYWON, DESERT BOTANICAL GARDEN, USA, LUCAS C. MAJURE, UNIVERSITY OF FLORIDA, USA, ILARIA N. COBB, ARIZONA STATE UNIVERSITY, USA, AMULYA BHASKARA, ARIZONA STATE UNIVERSITY, USA, JESÚS A. AVALOS-CALLEROS, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, GERARDO R. ARGÜELLO-ASTORGA, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, KARA SCHMIDLIN, ARIZONA STATE UNIVERSITY, USA, ANTHONY KHALIFEH, ARIZONA STATE UNIVERSITY, USA, KENDAL SMITH, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, MICHAEL C. LUND, ARIZONA STATE UNIVERSITY, USA, MATIAS KÖHLER, UFRGS, MARTIN F. WOJCIECHOWSKI, ARIZONA STATE UNIVERSITY, USA, WENDY C. HODGSON, DESERT BOTANICAL GARDEN, USA, RAUL PUENTE-MARTINEZ, DESERT BOTANICAL GARDEN, USA, KOENRAAD VAN DOORSLAER, UNIVERSITY OF ARIZONA, USA, SAFAA KUMARI, INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS (ICARDA), LEBANON, KEHINDE A. OYENIRAN, UNIVERSITY OF CAPE TOWN, SOUTH AFRICA, CHRISTIAN VERNIÈRE, CIRAD, FRANCE, DENIS FILLOUX, CIRAD, FRANCE, PHILIPPE ROUMAGNAC, CIRAD, FRANCE, PIERRE LEFEUVRE, CIRAD, FRANCE, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA P. KRABERGER, ARIZONA STATE UNIVERSITY, USA, DARREN P. MARTIN, UNIVERSITY OF CAPE TOWN, SOUTH AFRICA, ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA., University of Britsh Columbia [Vancouver], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Human Biology, and Faculty of Health Sciences
Subjects: 0106 biological sciences, 0301 basic medicine, Cactaceae, Phylogénie, [SDV]Life Sciences [q-bio], 01 natural sciences, Genome, Curtovirus, 2. Zero hunger, Diversity, biology, Phylogenetic tree, Opuntia, QR1-502, Infectious Diseases, Geminiviridae, Curly top, Cactus, Becurtovirus, food.ingredient, Pathologie végétale, Genome, Viral, Microbiology, Article, diversity, Hemiptera, 03 medical and health sciences, food, Virology, Animals, Virus classification, Géminivirus, Plant Diseases, H20 - Maladies des plantes, Virus des végétaux, biology.organism_classification, Recombination, recombination, Recombinaison, 030104 developmental biology, Evolutionary biology, 010606 plant biology & botany
Abstract: International audience; The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.
Published: 2021

29. Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America

Author: Pierre Lefeuvre, Gerardo R. Argüello-Astorga, Arvind Varsani, Simone G. Ribeiro, Simona Kraberger, Lucas C. Majure, Philippe Roumagnac, Jesús Aarón Avalos-Calleros, Ilaria N. Cobb, Kara Schmidlin, Amulya Bhaskara, Andrew M. Salywon, Rafaela S. Fontenele, Darren P. Martin, Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, University of Texas at Dallas [Richardson] (UT Dallas), School of Behavioral and Brain Sciences, University of Northern British Columbia [Prince George] (UNBC), Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), Desert Botanical Garden, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Embrapa Recursos Genéticos e Biotecnologia [Brasília], University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Structural Biology Research Unit [Cape Town], Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town-University of Cape Town, The molecular work was supported by a start-up grant awarded to AV from Arizona State University, USA., RAFAELA S. FONTENELE, Arizona State University, USA, AMULYA BHASKARA, Arizona State University, USA, ILARIA N. COBB, Arizona State University, USA, LUCAS C. MAJURE, University of Florida, Gainesville, USA, ANDREW M. SALYWON, Desert Botanical Garden, USA, JESÚS A. AVALOS-CALLEROS, Instituto Potosino de Investigación Científica y Tecnológica, Mexico, GERARDO R. ARGÜELLO-ASTORGA, Instituto Potosino de Investigación Científica y Tecnológica, Mexico, KARA SCHMIDLIN, Arizona State University, USA, PHILIPPE ROUMAGNAC, CIRAD, UMR PHIM, France, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA KRABERGER, Arizona State University, USA, DARREN P. MARTIN, University of Cape Town, South Africa, PIERRE LEFEUVRE, CIRAD, UMR PVBMT, France, ARVIND VARSANI, Arizona State University, USA., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], pseudo-recombination, Bemisia tabaci, 01 natural sciences, Plant Viruses, 2. Zero hunger, Recombination, Genetic, biology, Phylogenetic tree, food and beverages, Genomics, Plants, QR1-502, 3. Good health, Infectious Diseases, Phenotype, Geminiviridae, Begomovirus, Cucurbitaceae, Solanaceae, Whitefly, Genome, Viral, Microbiology, Virus, Article, 03 medical and health sciences, Pseudo-recombination, begomovirus, Virology, Botany, H20 - Maladies des plantes, Génome, Computational Biology, Virus des végétaux, Sequence Analysis, DNA, biology.organism_classification, Recombination, recombination, Recombinaison, 030104 developmental biology, Oleaceae, North America, 010606 plant biology & botany
Abstract: Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.
Published: 2021

30. Diversity, distribution and prevalence of vegetable‐infecting geminiviruses in Burkina Faso

Author: Edgar Valentin Traoré, Jean-Michel Lett, M. Hoareau, Oumar Traoré, Frédéric Chiroleu, Nicolas Barro, Fidèle Tiendrebeogo, Pierre Lefeuvre, A. S. Ouattara, Agathe Allibert, and Sohini Claverie
Subjects: 0106 biological sciences, 0301 basic medicine, Veterinary medicine, Distribution géographique, Géminivirus enroulement jaune tomat, viruses, Distribution (economics), Plant Science, Horticulture, Biology, 01 natural sciences, Virus, Plante légumière, 03 medical and health sciences, Mastrevirus, parasitic diseases, Pepper, Genetics, Pepper yellow vein Mali virus, Géminivirus, H20 - Maladies des plantes, Host (biology), business.industry, fungi, Begomovirus, food and beverages, Virus des végétaux, biology.organism_classification, 030104 developmental biology, Leaf curl, Biodiversité, business, Agronomy and Crop Science, geographic locations, 010606 plant biology & botany
Abstract: In West and Central Africa, as in many regions of the world, vegetables are severely affected by geminivirus diseases. In Burkina Faso, observation of various virus-like symptoms, especially on tomato, suggests the involvement of several geminiviruses and underlines the pressing need for additional information on their diversity, distribution, prevalence and host plant reservoirs. Large-scale surveys conducted in Burkina Faso confirmed the presence of tomato (yellow) leaf curl diseases (ToLCD-TYLCD) and geminiviruses in all localities with mean prevalences of 25% and 45%, respectively. Five geminiviruses including four begomoviruses (pepper yellow vein Mali virus (PepYVMLV), tomato leaf curl Burkina Faso virus, tomato leaf curl Mali virus and tomato leaf curl Ghana virus) and a dicot-infecting mastrevirus (chickpea chlorotic dwarf virus) were characterized on tomato. In addition, PepYVMLV and cotton leaf curl Gezira virus (CLCuGeV) were characterized on pepper and okra, respectively, in combination or not with alphasatellites and betasatellites for CLCuGeV. The most severe, prevalent and widely distributed virus on vegetables was PepYVMLV, which was characterized for the first time in combination with a genetically divergent DNA-B component that may constitute a key factor of PepYVMLV pathogenicity. Of the eight weeds identified as potential reservoir hosts of begomoviruses, four host PepYVMLV. The results confirm the importance of geminivirus diseases on vegetable crops in Burkina Faso and highlight the complex association of geminiviruses and satellites. The detection of begomoviruses in weeds growing close to crops points to the increasing necessity to consider reservoir plants and virus communities in the control of virus diseases.
Published: 2019

31. Novel circular DNA virus identified in

Author: Rafaela S, Fontenele, Matias, Köhler, Lucas C, Majure, Jesús A, Avalos-Calleros, Gerardo R, Argüello-Astorga, Fabián, Font, Andreza H, Vidal, Philippe, Roumagnac, Simona, Kraberger, Darren P, Martin, Pierre, Lefeuvre, and Arvind, Varsani
Subjects: Viral Proteins, Geminiviridae, Base Sequence, DNA, Viral, DNA Viruses, Opuntia, Amino Acid Sequence, Genome, Viral, DNA, Circular, Phylogeny, Plant Diseases
Abstract: Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus
Published: 2021

32. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

Author: Anthony Khalifeh, Christian Vernière, Kendal Smith, Michael C. Lund, Simona Kraberger, Kara Schmidlin, Rafaela S. Fontenele, Amulya Bhaskara, Darren P. Martin, Ilaria N. Cobb, Andrew M. Salywon, Arvind Varsani, Raul Puente-Martinez, Simone G. Ribeiro, Koenraad Van Doorslaer, Gerardo R. Argüello-Astorga, Martin F. Wojciechowski, Denis Filloux, Lucas C. Majure, Safaa G. Kumari, Matias Köhler, Jesús Aarón Avalos-Calleros, Pierre Lefeuvre, Philippe Roumagnac, Joshua Schreck, Wendy C. Hodgson, Arizona State University [Tempe] (ASU), Desert Botanical Garden, University of Florida [Gainesville] (UF), University of Northern British Columbia [Prince George] (UNBC), Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), International Center for Agricultural Research in the Dry Areas [Jordanie] (ICARDA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Embrapa Recursos Genéticos e Biotecnologia [Brasília], University of Cape Town, Arizona State University, USA, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, ANDREW M. SALYWON, DESERT BOTANICAL GARDEN, USA, LUCAS C. MAJURE, DESERT BOTANICAL GARDEN, USA, ILARIA N. COBB, ARIZONA STATE UNIVERSITY, USA, AMULYA BHASKARA, ARIZONA STATE UNIVERSITY, USA, JESÚS A. AVALOS-CALLEROS, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, GERARDO R. ARGÜLLO-ASTORGA, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, KARA SCHMIDLIN, ARIZONA STATE UNIVERSITY, USA, ANTHONY KHALIFEH, ARIZONA STATE UNIVERSITY, USA, KENDAL SMITH, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, MICHAEL C. LUND, ARIZONA STATE UNIVERSITY, USA, MATIAS KÖHLER, UFRGS, MARTIN F. WOJCIECHOWSKI, ARIZONA STATE UNIVERSITY, USA, WENDY C. HODGSON, DESERT BOTANICAL GARDEN, USA, RAUL PUENT-MARTINEZ, DESERT BOTANICAL GARDEN, USA, KOENRAAD VAN DOORSLAER, UNIVERSITY OF ARIZONA, USA, SAFAA KUMARI, ICARDA, CHRISTIAN VERNIÈRE, CIRAD, FRANCE, DENIS FILLOUX, CIRAD, FRANCE, PHILIPPE ROUMAGNAC, CIRAD, FRANCE, PIERRE LEFEUVRE, CIRAD, FRANCE, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA KRABERGER, ARIZONA STATE UNIVERSITY, USA, DARREN P. MARTIN, UNIVERSITY OF CAPE TOWNM, SOUTH AFRICA, and ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA.
Subjects: Cactaceae, 0106 biological sciences, 0301 basic medicine, Opuntia microdasys, [SDV]Life Sciences [q-bio], lcsh:QR1-502, SsDNA virus, 01 natural sciences, Genome, lcsh:Microbiology, ssDNA viruses [EN], Genus, Opuntioideae, Clade, Phylogeny, Cactoideae, Recombination, Genetic, Dactylopius, Geminiviridae, Infectious Diseases, ssDNA virus, Cactus, Geminivirus, cochineal insects, geminivirus, Genome, Viral, Biology, Article, Hemiptera, 03 medical and health sciences, Virology, Tobacco, Animals, Cochineal insects, Mexico, Géminivirus, Plant Diseases, H20 - Maladies des plantes, biology.organism_classification, United States, 030104 developmental biology, Evolutionary biology, 010606 plant biology & botany
Abstract: Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share &gt, 78.4% nucleotide identity with one another and &lt, 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
Published: 2020

33. Genome Resources of Three West African Strains of Pantoea ananatis Causing Bacterial Blight and Grain Discoloration of Rice

Author: Lucie Poulin, Ralf Koebnik, Kossi Kini, D. Silué, and Pierre Lefeuvre
Subjects: 0106 biological sciences, 0301 basic medicine, genome sequence, Pathologie végétale, Oryza sativa, Relation hôte pathogène, Plant Science, Biology, Agent pathogène, 01 natural sciences, Genome, 03 medical and health sciences, Pantoea ananatis, Molecular level, West Africa, parasitic diseases, Bacterial blight, Cultivar, H20 - Maladies des plantes, Genetics, Whole genome sequencing, Génome, rice pathogen, food and beverages, West african, 030104 developmental biology, H50 - Troubles divers des plantes, bacteriology, Erwiniaceae, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Members of the genus Pantoea have been reported as pathogens for many economically important crops, including rice. Little is known about their host−pathogen interactions at the molecular level and the lack of comprehensive genome data impedes targeted breeding strategies toward resistant rice cultivars. Here, we describe the structural and functional annotation of the draft genome sequences of three rice-pathogenic Pantoea ananatis strains, ARC272, ARC310, and ARC311, which were isolated in Burkina Faso, Togo, and Benin, respectively. The genome sequences of these strains will help in developing molecular diagnostic tools and provide new insight into common traits that may enable P. ananatis to infect rice.
Published: 2020

34. La proximité: Construction politique et expérience sociale

Author: Alain Bourdin, Marie-Pierre Lefeuvre, Annick Germain and Alain Bourdin, Marie-Pierre Lefeuvre, Annick Germain
Published: 2006

35. Espaces à saisir : interstices et communs urbains : La ville à l’épreuve de l’interdisciplinarité

Author: Didier Boisseuil, Ulrike Krampl, Marie-Pierre Lefeuvre, José Serrano, Didier Boisseuil, Ulrike Krampl, Marie-Pierre Lefeuvre, and José Serrano
Abstract: Toutes les villes, passées et présentes, comprennent des espaces ambigus, aux fonctions ou aux statuts incertains dont l'étude a longtemps été négligée. Qu'ils soient vides ou occupés, bâtis ou non, ces espaces semblent souvent à l'abandon mais sont aussi menacés, occupés, convoités. Ils peuvent (re)devenir communs ou cesser de l'être. Espaces à prendre, ils sont donc aussi à saisir intellectuellement. Prêter attention aux interstices urbains conduit à porter un regard neuf sur les dynamiques informelles, les régulations qui procèdent de l'usage, les processus d'institutionnalisation qui se soustraient à l'emprise de l'État. Cet ouvrage se propose donc de réfléchir à la jonction entre interstices et communs. Il réunit des spécialistes de la ville provenant de disciplines différentes (sociologie, géographie, histoire, histoire de l'art, droit, littérature, urbanisme…). La mise en regard de leurs travaux montre que l'interstice et le commun sont des prismes heuristiques pour appréhender les dynamiques urbaines dans l'espace et dans le temps.
Published: 2024

36. Tomato interveinal yellowing virus: A novel tomato-infecting monopartite begomovirus from Côte d'Ivoire

Author: Arthur Konan, Lassina Fondio, Thibaud Martin, Jocelin N’cho, Koutoua Séka, Noupé Diakaria Coulibaly, Pierre Lefeuvre, Jean-Michel Lett, and Murielle Hoareau
Subjects: Old World, Séquence nucléotidique, Biology, Virus, Crop, 03 medical and health sciences, Maladie des plantes, Solanum lycopersicum, Surveillance des cultures, Virology, Surveillance épidémiologique, Virus classification, 030304 developmental biology, H20 - Maladies des plantes, 0303 health sciences, Genetic diversity, Génome, Phylogenetic tree, 030306 microbiology, Begomovirus, fungi, Nucleic acid sequence, food and beverages, General Medicine, biology.organism_classification
Abstract: In this report, we present the first description of the complete genome sequences of a new monopartite begomovirus isolated from tomato with symptoms of interveinal yellowing of leaves collected in the region of Worodougou in the northwest of Cote d'Ivoire and provisionally named "tomato interveinal yellowing virus" (ToIYV). The DNA-A-like nucleotide sequences of ToIYV share the highest nucleotide sequence identity (83%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed that ToIYV is related to Old World monopartite begomoviruses. The discovery of a member of a new virus species on diseased tomato plants confirms the high genetic diversity in monopartite begomoviruses in West Africa and stresses the importance of maintaining epidemiological crop surveillance.
Published: 2021

37. Novel circular DNA virus identified in Opuntia discolor (Cactaceae) that codes for proteins with similarity to those of geminiviruses

Author: Arvind Varsani, Matias Köhler, Andreza H. Vidal, Philippe Roumagnac, Pierre Lefeuvre, Simona Kraberger, Jesús Aarón Avalos-Calleros, Gerardo R. Argüello-Astorga, Rafaela S. Fontenele, Lucas C. Majure, Fabián Font, and Darren P. Martin
Subjects: Infectivity, viruses, Nicotiana benthamiana, DNA virus, Biology, biology.organism_classification, Virology, Virus, chemistry.chemical_compound, Capsid, chemistry, Metagenomics, Homologous chromosome, DNA
Abstract: Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.
Published: 2021

38. Tomato interveinal yellowing virus: a novel tomato-infecting monopartite begomovirus from Côte d'Ivoire

Author: Jocelin, N'cho, Koutoua, Séka, Murielle, Hoareau, Arthur, Konan, Lassina, Fondio, Pierre, Lefeuvre, Thibaud, Martin, Noupe, Coulibaly, and Jean-Michel, Lett
Subjects: Cote d'Ivoire, Base Sequence, Solanum lycopersicum, Begomovirus, DNA, Viral, Phylogeny, Plant Diseases
Abstract: In this report, we present the first description of the complete genome sequences of a new monopartite begomovirus isolated from tomato with symptoms of interveinal yellowing of leaves collected in the region of Worodougou in the northwest of Côte d'Ivoire and provisionally named "tomato interveinal yellowing virus" (ToIYV). The DNA-A-like nucleotide sequences of ToIYV share the highest nucleotide sequence identity (83%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed that ToIYV is related to Old World monopartite begomoviruses. The discovery of a member of a new virus species on diseased tomato plants confirms the high genetic diversity in monopartite begomoviruses in West Africa and stresses the importance of maintaining epidemiological crop surveillance.
Published: 2020

39. Diverse genomoviruses representing twenty-nine species identified associated with plants

Author: Philippe Roumagnac, Denis Filloux, Pierre Lefeuvre, Natalia S. Lamas, Rayane A. Abreu, Darren P. Martin, A. L. Lacerda, James K. McCarthy, Lachlan S. Charles, Lucas C. Majure, Simone G. Ribeiro, Martin F. Wojciechowski, Simona Kraberger, Andrew M. Salywon, Arvind Varsani, Pauline Bernardo, Graciete B. Batista, Maketalena Aleamotu‘a, Gordon William Harkins, E. F. M. Abreu, Rafaela S. Fontenele, Daisy Stainton, Cécile Richet, Arizona State University [Tempe] (ASU), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Arkansas [Fayetteville], University of Newcastle [Australia] (UoN), University of the Western Cape, Manaaki Whenua – Landcare Research [Lincoln], University of California [Riverside] (UCR), University of California, Brazilian Agricultural Research Corporation (Embrapa), Embrapa Recursos Genéticos e Biotecnologia [Brasília], Desert Botanical Garden, University of Florida [Gainesville] (UF), University of Cape Town, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Embrapa (Brazil), National Council for Scientific and Technological Development (CNPq), CAPES, Next Generation Sonoran Desert Researchers (N-Gen), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Newcastle [Callaghan, Australia] (UoN), University of the Western Cape (UWC), University of California [Riverside] (UC Riverside), and University of California (UC)
Subjects: Identification, Indexage des virus des plantes, geminivirus, [SDV]Life Sciences [q-bio], Zoology, Genome, Viral, Genome, Gemycircularvirus, 03 medical and health sciences, South Africa, Phylogenetics, Virology, Opuntioideae, Phylogeny, Cactoideae, 030304 developmental biology, H20 - Maladies des plantes, 0303 health sciences, Génome, biology, 030306 microbiology, Genomoviridae, Australia, DNA Viruses, General Medicine, Virus des végétaux, Plants, biology.organism_classification, DNA Virus Infections, United States, 3. Good health, ssDNA virus, Metagenomics, France, cochineal insects, Brazil
Abstract: International audience; Genomoviruses (familyGenomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the generaGemykolovirus(n = 37),Gemyduguivirus(n = 9),Gemygorvirus(n = 8),Gemykroznavirus(n = 6),Gemycircularvirus(n = 21) andGemykibivirus(n = 17).
Published: 2020

40. How virulent are emerging maize-infecting mastreviruses?

Author: Arvind Varsani, Lara Donaldson, Penelope Hartnady, Jean-Michel Lett, Pierre Lefeuvre, Darren P. Martin, Sohini Claverie, Kehinde A. Oyeniran, Adérito L. Monjane, University of Cape Town, Institute of Infectious Disease & Molecular Medicine (IDM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Norwegian Veterinary Institute [Oslo], Arizona State University [Tempe] (ASU), School of Life Sciences (Arizona State University), Department of Integrative Biomedical Sciences [Cape Town], KAO was supported by the National Research Foundation (NRF) South Africa and The World Academy of Science (TWAS) Grant number 105461. SC, PL and J-ML were supported by the European Union (ERDF, contract GURDT I2016-1731-0006632), the Conseil Regional de La Reunion, the Agropolis Fondation (Labex Agro-Montpellier, E-SPACE project number 1504-004) and CIRAD., and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: endocrine system, medicine.medical_specialty, Genotype, viruses, Virulence, Pathologie végétale, Disease, Genome, Viral, Zea mays, Virus, Crop, 03 medical and health sciences, Mastrevirus, Maladie des plantes, Medical microbiology, Virology, Maize streak virus, medicine, neoplasms, Géminivirus, Phylogeny, H20 - Maladies des plantes, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, Géminivirus striure du maïs, biology, 030306 microbiology, General Medicine, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral
Abstract: International audience; Maize streak disease (MSD) is one of the most significant biotic constraints on the production of Africa's most important cereal crop. Until recently, the only virus known to cause severe MSD was the A-strain of maize streak virus (MSV/A), a member of the genus Mastrevirus, family Geminiviridae. However, over the past decade, two other mastreviruses, MSV/C and maize streak Reunion virus (MSRV), have been repeatedly found in the absence of MSV/A in maize plants displaying severe MSD symptoms. Here, we report on infectious clones of MSV/C and MSRV and test their ability to cause severe MSD symptoms. Although cloned MSV/C and MSRV genomes could cause systemic symptomatic infections in MSD-sensitive maize genotypes, these infections yielded substantially milder symptoms than those observed in the field. The MSV/C and MSRV isolates that we have examined are therefore unlikely to cause severe MSD on their own. Furthermore, mixed infections of MSRV and MSV/C with other mild MSV strains also consistently yielded mild MSD symptoms. It is noteworthy that MSRV produces distinctive striate symptoms in maize that are similar in pattern, albeit not in severity, to those seen in the field, showing that this virus may contribute to the severe MSD symptoms seen in the field. Therefore, despite not fulfilling Koch's postulates for MSV/C and MSRV as causal agents of severe MSD, we cannot exclude the possibility that these viruses could be contributing to currently emerging maize diseases.
Published: 2020

41. Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

Author: Olivier Pruvost, Claudine Boyer, Damien Richard, Francois Balloux, Pierre Lefeuvre, Adrien Rieux, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and University College of London [London] (UCL)
Subjects: 0301 basic medicine, 0106 biological sciences, Mutation rate, Gene Transfer, Horizontal, Population, Virulence, Single-nucleotide polymorphism, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Plasmid, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Gene, Pathogen, Phylogeny, Ecology, Evolution, Behavior and Systematics, Plant Diseases, 030304 developmental biology, 2. Zero hunger, education.field_of_study, 0303 health sciences, Bacteria, Phylogenetic tree, Effector, 15. Life on land, 030104 developmental biology, Evolutionary biology, Horizontal gene transfer, Chromosomal region, Genome, Bacterial, 010606 plant biology & botany
Abstract: Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. Such genes with essential functions include those involved in resistance to antimicrobial compounds and virulence factors in pathogenic bacteria. Understanding gene turnover at microevolutionary scales is critical to assess the pace of this evolutionary process. Here, we characterized and quantified gene turnover for the epidemic lineage of a bacterial plant pathogen of major agricultural importance worldwide. Relying on a dense geographic sampling spanning 39 years of evolution, we estimated both the dynamics of single nucleotide polymorphism accumulation and gene content turnover. We identified extensive gene content variation among lineages even at the smallest phylogenetic and geographic scales. Gene turnover rate exceeded nucleotide substitution rate by three orders of magnitude. Accessory genes were found preferentially located on plasmids, but we identified a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. Whereas most changes in the gene content are probably transient, the rapid spread of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens illustrates how some accessory genes can become ubiquitous within a population over short timeframes.
Published: 2020

42. Genome Resources of Three West African Strains of

Author: Kossi, Kini, Pierre, Lefeuvre, Lucie, Poulin, Drissa, Silué, and Ralf, Koebnik
Subjects: Pantoea, Oryza, Edible Grain, Genome, Bacterial, Plant Diseases
Abstract: Members of the genus
Published: 2020

43. Symptom evolution following the emergence of maize streak virus

Author: Anders Kvarnheden, Rémy Froissart, Shane L. Murray, Arvind Varsani, Daphné Linderme, Elham Yazdkhasti, Penelope Hartnady, Lara Donaldson, Darren P. Martin, Edward P. Rybicki, Betty E. Owor, Marc A. Suchard, Adérito Luis Monjane, Philippe Roumagnac, Philippe Lemey, Gordon William Harkins, Simon Dellicour, Kehinde A. Oyeniran, Pierre Lefeuvre, Rizwan A Syed, Marion Bezuidenhout, Dionne N. Shepherd, Norwegian Veterinary Institute [Oslo], Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Catholic University Leuven, Université libre de Bruxelles (ULB), University of Cape Town, Makerere University [Kampala, Ouganda] (MAK), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of the Western Cape (UWC), University of California [Los Angeles] (UCLA), University of California (UC), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University [Tempe] (ASU), Svenska Institutet : 00448/2014, Fonds de la Recherche Scientifique - FNRS, FWO, National Research Foundation - South Africa, World Academy of Sciences, European Union (EU), Conseil Regional de La Reunion, Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement, National Research Foundation - South Africa : TTK1207122745, European Union (EU) : PIOF-GA-2013-622571, European Research Council (ERC) : 725422, FWO : G066215N G0D5117N G0B9317N, Research Council of Norway : 267978/E40, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of the Western Cape, and University of California
Subjects: 0106 biological sciences, 0301 basic medicine, Évolution maligne, Résistance génétique, viruses, virus de la striure du maïs, maize, 01 natural sciences, F30 - Génétique et amélioration des plantes, Immunologie, Genotype, Maize streak virus, 2.2 Factors relating to the physical environment, pathogenicity, evolutionary trade-off, Aetiology, Biology (General), Pathogen, 2. Zero hunger, Genetics, biology, Phylogenetic tree, Transmission (medicine), General Neuroscience, Microbiology and Parasitology, General Medicine, Sciences bio-médicales et agricoles, Microbiologie et Parasitologie, Virus, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Host-Pathogen Interactions, Plant Necrosis and Chlorosis, Medicine, Infection, Research Article, Evolution, QH301-705.5, Pouvoir pathogène, Science, chlorosis, Virulence, Relation hôte pathogène, virus, 010603 evolutionary biology, Zea mays, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Transmission des maladies, H20 - Maladies des plantes, Plant Diseases, Evolutionary Biology, Géminivirus striure du maïs, General Immunology and Microbiology, Host (biology), Chlorose, evolutionary biology, Neurosciences cognitives, Molecular, biology.organism_classification, Maize, virulence, 030104 developmental biology, Biochemistry and Cell Biology, Microbiologie et protistologie [bacteriol.virolog.mycolog.]
Abstract: For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed. This demonstrates an evolutionary trade-off between amounts of pathogen-inflicted harm and how effectively viruses position themselves within plants to enable onward transmission., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2020

44. Author response: Symptom evolution following the emergence of maize streak virus

Author: Rémy Froissart, Shane L. Murray, Anders Kvarnheden, Dionne N. Shepherd, Marion Bezuidenhout, Gordon William Harkins, Lara Donaldson, Betty E. Owor, Marc A. Suchard, Daphné Linderme, Kehinde A. Oyeniran, Rizwan A Syed, Edward P. Rybicki, Adérito Luis Monjane, Penelope Hartnady, Philippe Lemey, Elham Yazdkhasti, Darren P. Martin, Arvind Varsani, Simon Dellicour, Philippe Roumagnac, and Pierre Lefeuvre
Subjects: Maize streak virus, Biology, biology.organism_classification, Virology
Published: 2020

45. Tomato leaf curl Kunene virus: a novel tomato-infecting monopartite begomovirus from Namibia

Author: Rolf W. Becker, Jean-Michel Lett, Vera De Cauwer, Jocelin N’cho, Marie Murielle Hoareau, Sohini Claverie, Pierre Lefeuvre, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: Sequence analysis, viruses, [SDV]Life Sciences [q-bio], Genome, Viral, Virus, 03 medical and health sciences, Solanum lycopersicum, Phylogenetics, Enroulement des feuilles, Virology, Surveillance épidémiologique, Phylogeny, Plant Diseases, 030304 developmental biology, H20 - Maladies des plantes, Whole genome sequencing, 0303 health sciences, Base Sequence, biology, Phylogenetic tree, 030306 microbiology, Begomovirus, fungi, Nucleic acid sequence, food and beverages, Sequence Analysis, DNA, General Medicine, Virus des végétaux, biology.organism_classification, Namibia, 3. Good health, DNA, Viral, Leaf curl
Abstract: International audience; This is the first description of the complete genome sequence of a new monopartite begomovirus isolated from tomato with symptoms of tomato (yellow) leaf curl disease collected in northwestern Namibia, which we provisionally name “tomato leaf curl Kunene virus”. The DNA-A-like nucleotide sequence shares the highest nucleotide sequence identity (82.8%) with tobacco leaf curl Zimbabwe virus (ToLCZWV). Phylogenetic analysis confirmed its affiliation with Old World monopartite begomoviruses. The discovery of a new begomovirus in a vegetable plant in Namibia highlights the importance of maintaining epidemiological surveillance in southern Africa.
Published: 2020

46. 14. La production de la ville au prisme de ses acteurs et de leurs activités : des recompositions à explorer

Author: Nadia Arab, Yasmina Dris, Marie-Pierre Lefeuvre, Mathieu Bonnefond, Yoan Miot, Laboratoire Architecture, Ville, Urbanisme, Environnement (LAVUE), Université Paris 8 Vincennes-Saint-Denis (UP8)-École nationale supérieure d'architecture de Paris-La Villette (ENSAPLV), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Nanterre (UPN)-École nationale supérieure d'architecture de Paris Val-de-Seine (ENSA PVDS)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN)-Ministère de la Culture (MC)-Université Paris 8 Vincennes-Saint-Denis (UP8)-École nationale supérieure d'architecture de Paris Val-de-Seine (ENSA PVDS)-École nationale supérieure d'architecture de Paris-La Villette (ENSAPLV)
Subjects: ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: ADISSON (F.), BARLES (S.), BLANC (N.), COUTARD (O.), FROUILLOU (L.), RASSAT (F.), Pour la recherche urbaine, CNRS Editions, Paris, 2020, pp 292 - 311.
Published: 2020

47. RDP3: a flexible and fast computer program for analyzing recombination.

Author: Darren P. Martin, Philippe Lemey, Martin Lott, Vincent Moulton, David Posada, and Pierre Lefeuvre
Published: 2010
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48. Ongoing geographical spread of Tomato yellow leaf curl virus

Author: Pierre Lefeuvre, Gordon William Harkins, John E. Thomas, Arvind Varsani, Simona Kraberger, Leendert J Cloete, Jean-Michel Lett, Andrew D. W. Geering, K. Bananej, Batsirai Mabvakure, Darren P. Martin, and Sharon van Brunschot
Subjects: 0301 basic medicine, Mediterranean climate, Phylogénie, Géminivirus enroulement jaune tomat, Distribution (economics), Solanum lycopersicum, Phylogeny, Recombination, Genetic, biology, Ecology, food and beverages, Phylogeography, Begomovirus, Modèle mathématique, S1, Séquence nucléotidique, Distribution géographique, Genome, Viral, Evolution, Molecular, 03 medical and health sciences, Virology, Botany, East Asia, Tomato yellow leaf curl virus, China, Plant Diseases, H20 - Maladies des plantes, Génie génétique, Génome, business.industry, Bayes Theorem, biology.organism_classification, 030104 developmental biology, Mutation, business
Abstract: Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing.
Published: 2016

49. Exploring the diversity of Poaceae infecting mastreviruses on Reunion Island using a viral metagenomicsbased approach

Author: Darren P. Martin, Pierre Lefeuvre, Murielle Hoareau, Sohini Claverie, Alassane Ouattara, Philippe Roumagnac, Arvind Varsani, Denis Filloux, Jean-Michel Lett, Pôle de Protection des Plantes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA), Institut de Recherche pour le Développement (IRD), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University [Tempe] (ASU), University of Cape Town, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union (EU) : GURDT I2016-1731-0006632, Conseil Regional de La Reunion, Agropolis Fondation (Labex Agro - Montpellier, E-SPACE project) : 1504-004, CIRAD, Agropolis Fondation (E-SPACE), Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Viral metagenomics, Virologie, lcsh:Medicine, Genome, 0302 clinical medicine, Maladie des plantes, lcsh:Science, Sanger sequencing, Multidisciplinary, Phylogenetic tree, Microbiology and Parasitology, High-throughput screening, High-Throughput Nucleotide Sequencing, Microbiologie et Parasitologie, Geminiviridae, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PCR, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, symbols, Genomics, Genome, Viral, Biology, Poaceae, Article, 03 medical and health sciences, symbols.namesake, Mastrevirus, Variation génétique, Phylogenetics, Virology, Plant Diseases, H20 - Maladies des plantes, Géminivirus striure du maïs, lcsh:R, Genetic Variation, Sequence Analysis, DNA, 030104 developmental biology, Metagenomics, Evolutionary biology, lcsh:Q, Reunion, 030217 neurology & neurosurgery
Abstract: Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
Published: 2019

50. Evolution and ecology of plant viruses

Author: Pierre Lefeuvre, Darren P. Martin, Philippe Roumagnac, Santiago F. Elena, Arvind Varsani, Dionne N. Shepherd, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), University of Cape Town, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Santa Fe Institute, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University [Tempe] (ASU), European Union (EU), Conseil Regional de La Reunion, Centre de Cooperation internationale en Recherche agronomique pour le Developpement (CIRAD), Spain Ministry of Science, Innovation and Universities-ERDF : BFU2015-65037-P, European Commission, Institut National de la Recherche Agronomique (France), and Ministerio de Economía y Competitividad (España)
Subjects: Viral metagenomics, F40 - Écologie végétale, Ecology (disciplines), viruses, Pathologie végétale, Biology, Microbiology, Plant Viruses, génomique, 03 medical and health sciences, Microbial ecology, Plant virus, genomic features [EN], Ecosystem, Transmission des maladies, Plant Diseases, H20 - Maladies des plantes, 2. Zero hunger, Ecological stability, 0303 health sciences, General Immunology and Microbiology, 030306 microbiology, Ecology, fungi, food and beverages, Plants, Biological Evolution, Infectious Diseases, Viral evolution, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Evolutionary ecology, Adaptation
Abstract: The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics., P.L. was supported by the European Union: European Regional Development Fund (ERDF), by the Conseil Régional de La Réunion and by the Centre de Coopération internationale en Recherche agronomique pour le Développement (CIRAD). S.F.E. was supported by a grant (BFU2015-65037-P) from Spain Ministry of Science, Innovation and Universities–ERDF.
Published: 2019

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